DESCRIPTION: “NCHS”
→ “National Center for Health Statistics (NCHS)” and “NDI” → “National
Death Index (NDI)”.DESCRIPTION.\dontrun{} with \donttest{}
in examples; all examples require CDC network access so none were
unwrapped.\d regex in NH_describe
documentation (unknown Rd macro on Windows); replaced with
[0-9].NHANES_2017_2020_MORT_2019_PUBLIC.dat;
has_lmf_public set to FALSE for that
cycle.cli pluralization crash in
nhanes_merge() when duplicate columns are found
({i} and {?s} quantity conflict resolved with
cli::qty()).\dontrun to \donttest: missing
cycles argument in nhanes_download_analyte()
calls; list passed to nhanes_mortality_link() instead of a
stacked data frame; undefined linked_data object in
nhanes_followup_summary() example.~ to file.path(tempdir(), "nhanesR"). This
prevents nhanesR from writing to the user’s home filespace without
explicit consent, in compliance with CRAN Policy. To retain a persistent
cache across sessions, set nhanesR.cache_dir in
~/.Rprofile.nhanes_cache_dir("~/my_nhanes_cache") example wrapped
in \dontrun{} to prevent directory creation during
R CMD CHECK.DESCRIPTION.inst/WORDLIST to suppress spell-check NOTEs for
domain abbreviations (NHANES, NCHS, LMF, NDI) and “codebook”.nhanes_harmonize(): the prefer_mgdl
argument has been replaced by
units = c("conventional", "SI", "both"). The default
("conventional") preserves prior behaviour; set
units = "SI" to retain SI columns and drop conventional
duplicates instead.Initial release.
nhanes_cycles() — list all continuous NHANES cycles
(1999–present) and optionally NHANES III (1988–1994), with cycle labels,
begin/end years, and file-name suffixes.
nhanes_manifest() — query the CDC data catalog for
available files within a given cycle and component.
nhanes_download() — download one or more NHANES XPT
files from CDC, parse them into R data frames, and cache them locally.
Falls back to foreign::read.xport() when
haven::read_xpt() cannot parse older files.
nhanes_stack() — row-bind per-cycle data frames into
a single data frame, filling columns absent in some cycles with
NA.
nhanes_merge() — join NHANES components by SEQN (and
optionally cycle), with survey-design-aware defaults.
nhanes_mortality_link() — download the NCHS
Public-Use Linked Mortality Files (LMF) for the relevant cycles and
left-join them onto an analytic dataset by SEQN. Mortality follow-up
runs through December 31, 2019.
nhanes_survival_prep() — prepare a survival analysis
dataset from a mortality-linked data frame: removes ineligible
participants (ELIGSTAT != 1), creates time and
event columns, optionally creates event_cause
for cause-specific mortality, and warns about asymmetric follow-up
across cycles.
nhanes_followup_summary() — summarize follow-up time
and event rates by cycle.
nhanes_ucod_labels() — return the 11-category ICD-10
underlying cause-of- death recode used in the public-use LMF.
nhanes_search_variables() — search the CDC NHANES
variable catalog for variables whose name or description matches a
keyword. Results are cached locally. The summarize argument
(default TRUE) collapses one-row-per-cycle output into one
row per unique variable name, with comma-separated file names, cycles,
and an n_cycles count.
nhanes_variable_map() — wraps
nhanes_search_variables() to return a single-row-per-cycle
lookup table (cycle, variable_name,
file_name) for a given analyte. Automatically drops
comment-code variables, prefers non-SI variables when both exist in a
cycle, and accepts a keep_vars argument to disambiguate
serum from urine forms of the same analyte (e.g. serum creatinine
vs. urinary creatinine).
nhanes_cache_dir() — view or change the local cache
directory.
Fixed CDC data file URLs: CDC reorganized all NHANES file paths
from /Nchs/Nhanes/{cycle}/ to
/Nchs/Data/Nhanes/Public/{begin_year}/DataFiles/. All
download functions updated accordingly.
Added Content-Type check in the HTTP download helper: CDC returns
HTTP 200 with an HTML error page when a file has moved;
nhanesR now detects this and aborts with an informative
message rather than saving a corrupt file.
Added foreign::read.xport() fallback for XPT files
that haven::read_xpt() cannot parse (affects some files
from NHANES cycles prior to 2003).
MD5 hash sidecar files (.md5) are written alongside
every cached RDS to detect corruption and trigger re-download when
needed.
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